Re: [gmx-users] entropy vs time plot

[lloyd riggs]

Yah but you'll have to smooth it, mean wise, or beter averidge several runs. qtiplot or equivalent will work (even MS Excell if you have the added mean determination formulas).

 

Stephan Watkins

 

Gesendet: Mittwoch, 21. Mai 2014 um 06:54 Uhr
Von: "tarak karmakar" <tarak20...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-us...@gromacs.org>
Betreff: Re: [gmx-users] entropy vs time plot

Hi Tsjerk,
Thanks for the quick reply.
I did the following

g_covar -f ../../npt_prod -s ../../npt_prod -n loop_II.ndx -o eigenval -v
eigenvec.trr -av average.pdb -b 0 -e 10000
g_anaeig -v eigenvec -entropy -temp 300 -b 0 -e 10000

What I want to plot is similar to this.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304994/figure/fig4/

Is there any flag for this?
I've checked g_covar -h and g_anaeig -h but didn't get the proper way.

Thanks,
Tarak



On Tue, May 20, 2014 at 11:04 PM, Tsjerk Wassenaar <tsje...@gmail.com>wrote:

> Hi Tarak,
>
> You will have to use -b/-e to set the start and end times.
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, May 20, 2014 at 12:18 PM, tarak karmakar <tarak20...@gmail.com
> >wrote:
>
> > Dear All,
> > Could anyone tell me how to plot configurational entropy as a function of
> > simulation time?
> > Do I need to manually specify the -dt(say after each 1 ns) during the
> > g_covar and then do g_anaeig in each of the step?
> >
> > thanks,
> > Tarak
> > --
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> Tsjerk A. Wassenaar, Ph.D.
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